Summary of the invention
The present invention seeks to overcome the defect that prior art can not detect multiple infectious disease pathogenic agent simultaneously, a kind of method that the infectious disease pathogens that may be present in biological sample are detected be provided, comprising:
(i) nucleic acid fragment of amplification biological sample, described nucleic acid fragment is the combination of following one or more:
The nucleic acid fragment as shown in SEQ ID NO.1 of the outer membrane protein A gene of Chlamydia pneumoniae;
The nucleic acid fragment as shown in SEQ ID NO.2 of OMP26 P6 gene;
The nucleic acid fragment as shown in SEQ ID NO.3 of mycoplasma pneumoniae attachment proteins P1 gene;
The nucleic acid fragment as shown in SEQ ID NO.4 of pneumolysin gene;
The scavenger cell of bacillus legionnaires,pneumophila infects the nucleic acid fragment as shown in SEQ ID NO.5 of Enhancin gene;
(ii) with probe, detect a kind of specific hybrid in described probe and step (i) amplified production.
A preferred embodiment of the present invention is the nucleic acid fragment that described step (i) is utilized NASBA technology amplification sample.The preferred operational conditions of NASBA is 41 ℃~45 ℃ incubations 90~150 minutes.
In step of the present invention (ii), preferably the hybridization of described probe and step (i) gained amplified production is carried out on solid support.
Can stationary probe and one or more of nucleic acid fragment, for example, be fixed on Sptting plate.Term " solid support " refers to and keeps the solid substrate that oligonucleotide probe under its hybridization characteristic prerequisite can coupling, and conventionally, solid substrate is nylon end, cellulose membrane, microballon, chip or Sptting plate.Before fixing, can modify probe, to promote fixing or raising hybridization efficiency.Such modification comprises homopolymeric tailing, with NH
2group or vitamin H, hapten conjugation.
Or probe and nucleic acid fragment are all unfixed, hybridization can be carried out in liquid medium, and its detection can be carried out with flow cytometry.
The primer that the present invention also provides step (i) to use, its nucleotide sequence is as follows:
The 1st group of primer is used for the nucleic acid fragment increasing as shown in SEQ ID NO.1, and its upstream primer nucleotide sequence is as shown in SEQ ID NO.6, and its downstream primer nucleotide sequence is as shown in SEQ ID NO.7;
The 2nd group of primer is used for the nucleic acid fragment increasing as shown in SEQ ID NO.2, and its upstream primer nucleotide sequence is as shown in SEQ ID NO.9, and its downstream primer nucleotide sequence is as shown in SEQ ID NO.10;
The 3rd group of primer is used for the nucleic acid fragment increasing as shown in SEQ ID NO.3, and its upstream primer nucleotide sequence is as shown in SEQ ID NO.12, and its downstream primer nucleotide sequence is as shown in SEQ ID NO.13;
The 4th group of primer is used for the nucleic acid fragment increasing as shown in SEQ ID NO.4, and its upstream primer nucleotide sequence is as shown in SEQ ID NO.15, and downstream primer nucleotide sequence is as shown in SEQ ID NO.16;
The 5th group of primer is used for the nucleic acid fragment increasing as shown in SEQ ID NO.5, and its upstream primer nucleotide sequence is as shown in SEQ ID NO.18, and downstream primer nucleotide sequence is as shown in SEQ ID NO.19.
Above-mentioned the 1st group to the 5th group primer be corresponding Chlamydia pneumoniae, hemophilus influenzae, mycoplasma pneumoniae, streptococcus pneumoniae, the bacillus legionnaires,pneumophila of detecting respectively.
In actual applications, also having a kind of may be any one or more than one the combination of using in above-mentioned primer group, increase and detect a certain or several in Chlamydia pneumoniae, hemophilus influenzae, mycoplasma pneumoniae, streptococcus pneumoniae and bacillus legionnaires,pneumophila, as using the sequence of the 1st group and the 4th group to carry out detection of Chlamydia pneumoniae and streptococcus pneumoniae etc.
The capture probe that the present invention also provides described step (ii) to use, its nucleotide sequence is as shown in SEQ IDNO.21, and what it was direct or indirect is connected on solid support, and hybridizes with step (i) gained amplified production.
The present invention also provides the detection probes of using in step (ii):
Sequence 1, as shown in SEQ ID NO.8, detects the nucleic acid fragment as shown in SEQ ID NO.1;
Sequence 2, as shown in SEQ ID NO.11, detects the nucleic acid fragment as shown in SEQ ID NO.2;
Sequence 3, as shown in SEQ ID NO.14, detects the nucleic acid fragment as shown in SEQ ID NO.3;
Sequence 4, as shown in SEQ ID NO.17, detects the nucleic acid fragment as shown in SEQ ID NO.4;
Sequence 5, as shown in SEQ ID NO.20, detects the nucleic acid fragment as shown in SEQ ID NO.5.
Above-mentioned sequence 1~5 is corresponding Chlamydia pneumoniae, hemophilus influenzae, mycoplasma pneumoniae, streptococcus pneumoniae, the bacillus legionnaires,pneumophila detecting after amplification respectively.
Detection probes can detect with multiple biological method.Preferably, described detection probes, by vitamin H or digoxigenin labeled, adds substrate, reads absorbance carry out result judgement through termination reaction step by spectrophotometer.
The present invention preferably embodiment is to carry out at one time the described detecting step of step (ii) by a plurality of reaction tubess, and the detection probes that each reaction tubes is used should detect the existence of a certain pathogenic agent to a kind of in sequence 5 and with the primer pair that step (i) is used jointly for sequence 1.
The absorbancy result treatment of aforesaid method can be taked following scheme: a tested K negative control sample, get its absorbance, determine as follows threshold value: m+K * SD, the negative contrast absorbancy of m arithmetical av, the negative contrast absorbancy of SD standard deviation, K determines according to different experimental conditions, as the colony's number or the sample number that detect.Detection reading is greater than threshold value and is judged to be detected result " positive "; Detection reading is less than threshold value and is judged to be detected result " feminine gender ".
Term of the present invention " primer " refers to the single stranded oligonucleotide sequence as the initiation site of synthetic primer extension products, and it is complementary with nucleic acid chains to be copied, and length and sequence must be suitable for the synthetic of extension products.
Term of the present invention " probe " refers to single stranded oligonucleotide, for nucleic acid fragment specific hybrid." specific hybrid " refers to that the whole region of described probe and nucleic acid or a part are forming duplex under specific experiment condition, and under these conditions, described probe not with detected sample in other nucleic acid of existing or other regions of nucleic acid form duplexs.
After probe and nucleic acid fragment hybridization, can be by the mode of any appropriate, the detection of hybridizing, the label probe that for example can detect and/or nucleic acid fragment, for auxiliary detection, preferably target nucleic acid fragment carries out NASBA amplification or pcr amplification.
The present invention also provides a kind of test kit that the infectious disease pathogens that may be present in biological sample are detected, its comprise outer membrane protein A gene for the Chlamydia pneumoniae that increases as shown in SEQ ID NO.1 nucleic acid fragment primer, primer for the OMP26 P6 gene nucleic acid fragment as shown in SEQ ID NO.2 that increases, primer for the mycoplasma pneumoniae attachment proteins P1 gene nucleic acid fragment as shown in SEQ ID NO.3 that increases, for the primer of the pneumolysin gene nucleic acid fragment as shown in SEQ ID NO.4 that increases with infect a group or more combination of the primer of Enhancin gene nucleic acid fragment as shown in SEQ ID NO.5 for the scavenger cell of the bacillus legionnaires,pneumophila that increases.
Preferably, the primer of test kit of the present invention is selected from following 5 groups of primers:
The 1st group of primer is used for the nucleic acid fragment increasing as shown in SEQ ID NO.1, and its upstream primer nucleotide sequence is as shown in SEQ ID NO.6, and its downstream primer nucleotide sequence is as shown in SEQ ID NO.7;
The 2nd group of primer is used for the nucleic acid fragment increasing as shown in SEQ ID NO.2, and its upstream primer nucleotide sequence is as shown in SEQ ID NO.9, and its downstream primer nucleotide sequence is as shown in SEQ ID NO.10;
The 3rd group of primer is used for the nucleic acid fragment increasing as shown in SEQ ID NO.3, and its upstream primer nucleotide sequence is as shown in SEQ ID NO.12, and its downstream primer nucleotide sequence is as shown in SEQ ID NO.13;
The 4th group of primer is used for the nucleic acid fragment increasing as shown in SEQ ID NO.4, and its upstream primer nucleotide sequence is as shown in SEQ ID NO.15, and downstream primer nucleotide sequence is as shown in SEQ ID NO.16;
The 5th group of primer is used for the nucleic acid fragment increasing as shown in SEQ ID NO.5, and its upstream primer nucleotide sequence is as shown in SEQ ID NO.18, and downstream primer nucleotide sequence is as shown in SEQ ID NO.19.
Preferably, test kit of the present invention also comprises the capture probe as shown in nucleotide sequence SEQ ID NO.21.
More preferably, test kit of the present invention also comprises the detection probes that following at least one and primer pair are answered:
Sequence 1, as shown in SEQ ID NO.8, detects the nucleic acid fragment as shown in SEQ ID NO.1;
Sequence 2, as shown in SEQ ID NO.11, detects the nucleic acid fragment as shown in SEQ ID NO.2;
Sequence 3, as shown in SEQ ID NO.14, detects the nucleic acid fragment as shown in SEQ ID NO.3;
Sequence 4, as shown in SEQ ID NO.17, detects the nucleic acid fragment as shown in SEQ ID NO.4;
Sequence 5, as shown in SEQ ID NO.20, detects the nucleic acid fragment as shown in SEQ ID NO.5.
Test kit of the present invention can also comprise one or more following components:
Hybridization buffer or prepare the specification sheets of described hybridization buffer; Washing soln or prepare the specification sheets of described washing soln; Detect the component of the crossbred forming; For probe is attached to the component on solid support.
The method that the infectious disease pathogens that may be present in biological sample are detected of the present invention, the advantage of contrast prior art is:
(1) detection speed is fast, and efficiency is high, can be as required, and double, triple or Multiple Combination detects multiple infective pathogen body simultaneously at random, also can detect single pathogenic agent;
(2) highly sensitive, it is 10 that NASBA can detect viral Cmin
-11pM, higher than the susceptibility of classical pathogen separation method;
(3) high specificity, because external double-stranded DNA is without T7 promoter sequence, can not be amplified, and this has just significantly improved the specificity of NASBA reaction; Due to the primer in amplification procedure and the probe dual function in testing process, again guaranteed the specificity of pathogen detection, and the reaction conditions of NASBA is gentle, and shorter than the time of PCR reaction needed, therefore transcribe more faithful to template, further reduced mispairing rate;
(4) simple to operate, result is stable, and whole testing process only needs the instrument of this routine of microplate reader;
(5) be applicable to early diagnosis, be applicable to the early stage rapid detection of great communicate illness that FUO causes, the random combine of multiple pathogens detects and the check of a large amount of samples.
(6) applied widely, sampling is simple.In sample, the pollution of DNA, heparin, EDTA, Citrate trianion, oxyphorase, albumin and lipid etc. will can not impact result, thereby is applicable to various samples to be checked as brush,throat, ight soil, blood etc.
Embodiment
Below in conjunction with specific embodiment, further set forth the present invention.These embodiment are only not used in and limit the scope of the invention for the present invention is described, those skilled in the art can carry out various transformations and modification to it, and these equivalent form of values fall into protection scope of the present invention equally.
The experimental technique of unreceipted actual conditions in embodiment below, conventionally according to normal condition, or the condition of advising according to manufacturer.
Embodiment 1
Design and prepare primer, probe sequence.
According to NCBI search, choose the specific gene sequence of Chlamydia pneumoniae, hemophilus influenzae, mycoplasma pneumoniae, pneumonia streptococcus, bacillus legionnaires,pneumophila, they respectively:
The outer membrane protein A gene sequence of Chlamydia pneumoniae, GENEBANK accession number is AY555078, choose sequence high conservative part as target nucleic acid sequence, the target sequence that the present invention chooses is outer membrane protein A gene 660-893, and its nucleotide sequence is as shown in SEQ ID NO.1;
OMP26 P6 gene order, GENEBANK accession number is M19391, and the target nucleic acid sequence that the present invention chooses is the 173-372 of outer membrane protein P6 gene, and its nucleotide sequence is as shown in SEQID NO.2;
Mycoplasma pneumoniae attachment proteins P1 gene order, GENEBANK accession number is M21519, and the target nucleic acid sequence that the present invention chooses is the 3667-3780 of Nucleocapsid Protein Gene, and its nucleotide sequence is as shown in SEQID NO.3;
Pneumolysin gene order, GENEBANK accession number is M17717, and the target nucleic acid sequence that the present invention chooses is the 464-623 of Nucleocapsid Protein Gene, and its nucleotide sequence is as shown in SEQ IDNO.4;
The scavenger cell of bacillus legionnaires,pneumophila infects Enhancin gene order, GENEBANK accession number is AF095230, the target nucleic acid sequence that the present invention chooses is the 406-563 that scavenger cell infects Enhancin gene gene, and its nucleotide sequence is as shown in SEQ ID NO.5;
Analyze the information of above-mentioned virus-specific gene, eliminating through carry out between primer/interdimers of sequence analysis software DNAman, and through the specificity of BLAST checking primer and with the homology of close pathogenic agent, design NASBA primer and probe for above-mentioned pathogen detection.
The nucleotide sequence of capture probe is as shown in SEQ ID NO.21;
The detection probes of primer and correspondence is as follows:
The 1st group: the upstream primer nucleotide sequence of the nucleic acid fragment for the outer membrane protein A gene of the Chlamydia pneumoniae that increases as shown in SEQ ID NO.1 as shown in SEQ ID NO.6, downstream primer nucleotide sequence as shown in SEQ ID NO.7, detection probes is as shown in SEQ ID NO.8;
The 2nd group: for the upstream primer nucleotide sequence of the nucleic acid fragment of OMP26 P6 gene as shown in SEQ ID NO.2 that increase as shown in SEQ ID NO.9, downstream primer nucleotide sequence as shown in SEQ ID NO.10, detection probes is as shown in SEQ ID NO.11;
The 3rd group: for the upstream primer nucleotide sequence of the nucleic acid fragment of mycoplasma pneumoniae attachment proteins P1 gene as shown in SEQ ID NO.3 that increase as shown in SEQ ID NO.12, downstream primer nucleotide sequence as shown in SEQ ID NO.13, detection probes is as shown in SEQ ID NO.14;
The 4th group: for the upstream primer nucleotide sequence of the nucleic acid fragment of pneumolysin gene as shown in SEQ ID NO.4 that increase as shown in SEQ ID NO.15, downstream primer nucleotide sequence as shown in SEQID NO.16, detection probes is as shown in SEQ ID NO.17;
The 5th group: the upstream primer nucleotide sequence that infects the nucleic acid fragment of Enhancin gene as shown in SEQ IDNO.5 for the scavenger cell of the bacillus legionnaires,pneumophila that increases as shown in SEQ ID NO.18, downstream primer nucleotide sequence as shown in SEQ ID NO.19, detection probes is as shown in SEQ ID NO.20.
Embodiment 2
Prepare test kit of the present invention.Consist of:
1, amplification system
Every group of 10uM of primer (5 groups)
Tris/HCl 10-100mM
Repone K 1-10mM
BSA 1-5g/ml
Dithiothreitol (DTT) 1-5mM
Nucleoside triphosphate and deoxidation nucleoside triphosphate isoconcentration mixture 200-1000uM
ThermoScript II 5-300U
Ribonuclease H RNase H 5-300U
Phage t7 ribonucleic acid polymerase 5-300U
Negative control is without RNA enzyme water
Positive control is avian influenza virus H5 hypotype HA gene order, avian influenza virus H7 hypotype HA gene, the Nucleocapsid Protein Gene of sars coronavirus, Hantavirus nucleocapsid protein gene order, Ye Shi plague bacillus pPCP1 gene order, the anthrax bacillus putative protein gene order of 5pM synthetic.
2, detection system
Detection probes (5 groups, by digoxigenin labeled) 26 μ M
Capture probe (biotin labeling) 26 μ M
Cleaning buffer solution 1xTBS
Hybridization buffer 10mg/ml BSA, 50mM Tris-HCl (pH 7.5)
Detect damping fluid 1xTBS:1.4M NaCl, 30mM KCl, 260mM
Detect the antibody of the anti-digoxin of concentrated solution alkali phosphatase enzyme mark
Stop buffer 3M NaOH
Substrate 10mM para-nitro-pheneye phosphate solution
Negative control is without RNA enzyme water;
Positive control is that outer membrane protein A gene sequence, OMP26 P6 gene order, mycoplasma pneumoniae attachment proteins P1 gene order, the pneumolysin gene order of the Chlamydia pneumoniae of 5pM synthetic are, the scavenger cell of bacillus legionnaires,pneumophila infects Enhancin gene order.
Embodiment 3:
The method that the infectious disease pathogens that may be present in biological sample are detected is also the using method of test kit of the present invention simultaneously.
1, nucleic acid extraction
Get sputum sample to be measured, centrifuging and taking supernatant, add 1ml guanidinium isothiocyanate, after mixing, add again 1ml TRIZOL, vibration mixes, in ice bath, place 5 minutes. add 350ul chloroform, fully vibration mixes, after static layering, immediately in 4 ℃, centrifugal 20 minutes of 12000r/min. supernatant is transferred to another centrifuge tube, add isopyknic Virahol (4 ℃ of precoolings) and mix .-20 ℃ of placement 1h, 4 ℃, 12000r/ minute centrifugal 20 minutes, precipitation is that total RNA. adds 0.5ml 75% washing with alcohol, 4 ℃, 12000r/ minute centrifugal 10 minutes, carefully outwell ethanol, room temperature is placed 10 minutes, add appropriate DEPC treated water dissolution precipitation, obtain determined nucleic acid sample,-80 ℃ save backup.
2, NASBA amplified reaction
20 μ l NASBA amplification reaction systems shown in being formulated as follows in sterilizing centrifuge tube at 0.5ml without RNA enzyme, 41 ℃ of incubations 90 minutes, nucleic acid amplification product was for subsequent detection.
The final concentration of NASBA amplification reaction system (20 μ l) is specially:
Determined nucleic acid sample 200 μ M
Primer 1 μ M
AMV 10U
RNase H 10U
T7 RNA polymerase 10U
Tris/HCl 10mM
Repone K 1mM
BSA 100mg/ml
Dithiothreitol (DTT) 1mM
Nucleoside triphosphate and deoxidation nucleoside triphosphate isoconcentration mixture 200uM
3, NASBA amplified production detects
Get step 2 gained 5 μ l NASBA products, add 1 μ l detection probes solution (every hole adds a kind of) and 1 μ l capture probe solution, after mixing with 43 μ l hybridization buffers, add be coated with streptavidin microwell plate (purchased from Thermo fisher scientific) each independently in hole, 45 ℃ of incubations 1 hour, with 250 μ l 1xTBS, pH 7.4 cleans aperture three times.Incline after solution at every turn and will pat dry microwell plate, every hole adds the mixture (by detecting concentrated solution: detect damping fluid=1: 500 dilute) that 100 μ l detect damping fluid and detect concentrated solution, detect concentrated solution purchased from Sigma, P/N N7653, at room temperature incubation is 30 minutes, with 250 μ l 1xTBS, pH 7.4 cleans aperture three times, incline after solution at every turn and will pat dry microwell plate, micropore adds 100 μ l substrates, lucifuge room temperature incubation 5 minutes, 100 μ l stop buffers also shake color development stopping reaction gently, microwell plate and microwell plate sheet frame are put into standard 96 hole microwell plate spectrophotometers and read 405nm absorbancy.100 μ l substrates add 100 μ l stop buffer references as a setting.
4, Analysis of test results
Above-mentioned absorbancy result treatment is taked following scheme: test 8 its absorbances of negative control sample determination, determine as follows threshold value: m+8 * SD, the negative contrast absorbancy of m arithmetical av, the negative contrast absorbancy of SD standard deviation.Threshold value is 0.15+0.035 * 8=0.43.Detection reading is greater than threshold value and is judged to be " positive "; Detection reading is less than threshold value and is judged to be " feminine gender ".
Embodiment 4:
The method that the infectious disease pathogens that may be present in biological sample are detected is also the using method of test kit of the present invention simultaneously.
1, nucleic acid extraction
Get blood sample to be measured, get fresh whole blood 2ml and add 1ml 3% Trisodium Citrate, mix latter 4 ℃, 3000r/ minute centrifugal, 10 minutes, get supernatant, add 1ml guanidinium isothiocyanate, after mixing, add again 1ml TRIZOL, vibration mixes, in ice bath, place 5 minutes. add 350ul chloroform, fully vibration mixes, after static layering, immediately in 4 ℃, 12000r/ minute is centrifugal 20 minutes. supernatant is transferred to another centrifuge tube, add isopyknic Virahol (4 ℃ of precoolings) and mix .-20 ℃ of placement 1h, 4 ℃, centrifugal 20 minutes of 12000r/min, precipitation is that total RNA. adds 0.5ml 75% washing with alcohol, 4 ℃, centrifugal 10 minutes of 12000r/min, carefully outwell ethanol, room temperature is placed 10 minutes, add appropriate DEPC treated water dissolution precipitation, obtain determined nucleic acid sample,-80 ℃ save backup.
2, NASBA amplification
20 μ l NASBA amplification reaction systems shown in being formulated as follows in sterilizing centrifuge tube at 0.5ml without RNA enzyme, 41 ℃ of incubations 90 minutes, nucleic acid amplification product was for subsequent detection.
The final concentration of NASBA amplification reaction system (20 μ l) is specially:
Determined nucleic acid sample 600uM
Primer 2 uM
AMV 150U
RNase H 150U
T7 RNA polymerase 150U
Tris/HCl 10mM
Repone K 1mM
BSA 200mg/ml
Dithiothreitol (DTT) 3mM
Nucleoside triphosphate and deoxidation nucleoside triphosphate isoconcentration mixture 600uM
3, NASBA amplified production detects
Get step 2 gained 5 μ l NASBA products, add 1 μ l detection probes solution (every hole adds a kind of) and 1 μ l capture probe solution, mix with 43 μ l hybridization buffers and add be coated with streptavidin microwell plate (purchased from Thermo fisher scientific company) each independently in hole, 45 ℃ of incubations 1 hour, with 250 μ l 1xTBS, pH 7.4 cleans aperture three times.Incline after solution at every turn and will pat dry microwell plate, every hole adds 100 μ l and detects damping fluid and the mixture (by detecting concentrated solution: detect damping fluid=1: 500 configure) that detects damping fluid, at room temperature incubation is 30 minutes, with 250 μ l 1xTBS, pH7.4 cleans aperture three times, incline after solution at every turn and will pat dry microwell plate, micropore adds 100 μ l 10mM Tris/HCl, lucifuge room temperature incubation 5 minutes, add 100 μ l stop buffers and shake gently color development stopping reaction, microwell plate and microwell plate sheet frame are put into standard 96 hole microwell plate spectrophotometers and read 405nm absorbancy, use 100 μ l 10mM Tris/HCl to add 100 μ l stop buffer references as a setting.
While whether containing certain 3 kinds of pathogenic agent in detecting testing sample, only need when preparation amplification system, add this 3 kinds of primers that pathogenic agent is corresponding respectively at 3 reaction tubess, add this 3 kinds of probe solutions that pathogenic agent is corresponding during detection, other steps are same.
4, Analysis of test results
The absorbancy of measuring 10 known negative samples, threshold value is m (negative control absorbancy arithmetical av)+10 * SD (negative control absorbancy standard deviation), threshold value is generally 0.15+0.03 * 10=0.45.Detection reading is greater than threshold value and is judged to be detected result " positive "; Detection reading is less than threshold value and is judged to be detected result " feminine gender ".
Embodiment 5: the sensitivity experiment that detects bacillus legionnaires,pneumophila
1, nucleic acid amplification
Get 1ml bacillus legionnaires,pneumophila standard substance and add 1ml guanidinium isothiocyanate, after mixing, add again 1mlTRIZOL, vibration mixes, in ice bath, place 5 minutes. add 350ul chloroform, fully vibration mixes, after static layering, immediately in 4 ℃, centrifugal 20 minutes of 12000r/min. supernatant is transferred to another centrifuge tube, add isopyknic Virahol (4 ℃ of precoolings) and mix .-20 ℃ of placement 1h, 4 ℃, centrifugal 20 minutes of 12000r/min, precipitation is that total RNA. adds 0.5ml 75% washing with alcohol, 4 ℃, centrifugal 10 minutes of 12000r/min, carefully outwell ethanol, room temperature is placed 10 minutes, add appropriate DEPC treated water dissolution precipitation, obtain determined nucleic acid sample, measure its concentration.
0.5ml without the sterilizing centrifuge tube of RNA enzyme in mark respectively, 20 μ lNASBA amplification reaction systems shown in being formulated as follows, and two negative controls are set simultaneously, bacillus legionnaires,pneumophila RNA is formulated as 10
-9pm, 10
-10pm, 10
-11pm, 10
-12the final concentration of pm, every kind of concentration arranges multiple pipe, usings without RNA enzyme water as negative control, 41 ℃ of water-baths 95 minutes.Nucleic acid amplification product is for subsequent detection.
The final concentration of NASBA amplification reaction system (20 μ l) is specially:
Bacillus legionnaires,pneumophila RNA
Primer (the 5th group) 1 μ M
AMV 10U
RNase H 10U
T7 RNA polymerase 10U
Tris/HCl 10mM
Repone K 1mM
BSA 100mg/ml
Dithiothreitol (DTT) 1mM
Nucleoside triphosphate and deoxidation nucleoside triphosphate isoconcentration mixture 200uM
Get amplified production and entrust Shanghai Sangon Biological Engineering Technology And Service Co., Ltd to carry out sequential analysis, its nucleotide sequence is as shown in SEQ ID NO.5, consistent with the scavenger cell infection Enhancin gene 406-563 section of bacillus legionnaires,pneumophila.
2, detection of nucleic acids
1) supporting to lay a microwell plate lath on sheet frame, this coated in microporous plate streptavidin (purchased from Thermo fisher scientific company).
2) in each micropore, add successively 43 μ l hybridization buffers, add 1 μ l detection probes solution (the 5th group) and 1 μ l capture probe solution, 5 μ l amplified productions, rap supporting plate with mixing solutions (attention avoids producing bubble).
3) firmly cover sealed membrane and avoid evaporation, 45 ℃ of water-baths 60 minutes.
4) incline after solution, with 250 μ l 1xTBS, pH 7.4 cleans aperture five times, and cleans 30s at every turn, after the solution that inclines, pats dry microwell plate.
5) every hole adds the mixture (by detecting concentrated solution: damping fluid=1: 500 configure) of 100 μ l detection damping fluids and detection concentrated solution, firmly covers sealed membrane and avoids evaporation.
6) incubation 30 minutes at room temperature.
7) incline after solution, with 250 μ l 1xTBS, pH 7.4 cleans aperture five times, and cleans 30s at every turn, after the solution that at every turn inclines, pats dry microwell plate.
8) micropore adds 100 μ l connecting fluids (carefully avoiding introducing foam in hole).
9) lucifuge room temperature incubation is 5 minutes.
10) micropore adds 100 μ l stop buffers and shakes gently color development stopping reaction.
11) microwell plate and microwell plate sheet frame are put into standard 96 hole microwell plate spectrophotometers and read 405nm absorbancy.
3, result is as shown in table 1.
Table 1. the method for the invention detects the absorbance of different concns bacillus legionnaires,pneumophila (Lp)
Sample |
Lp |
Lp |
Lp |
Lp |
Lp |
Lp |
Lp |
Lp |
Without RNA enzyme water |
Without RNA enzyme water |
Concentration pM |
10
-9 |
10
-9 |
10
-10 |
10
-10 |
10
-11 |
10
-11 |
10
-12 |
10
-12 |
|
|
OD value 405nm |
1.144 |
1.091 |
0.869 |
0.863 |
0.529 |
0.572 |
0.286 |
0.341 |
0.199 |
0.212 |
4, interpretation of result
Through spectrophotometer, read absorbance and carry out result judgement, measure the absorbancy of 7 known negative samples (water), threshold value is m (negative control absorbancy arithmetical av)+7 * SD (negative control absorbancy standard deviation), and threshold value is 0.17+0.04 * 7=0.45.Detection reading is greater than threshold value and is judged to be detected result " positive "; Detection reading is less than threshold value and is judged to be detected result " feminine gender ".Be that the minimum concentration that the primer of group 2 and the detection probes of group 2 can detect bacillus legionnaires,pneumophila is 10
-11pM.
Embodiment 6: the sensitivity experiment that detects other pathogenic agent
With reference to embodiment 5, Chlamydia pneumoniae, hemophilus influenzae, mycoplasma pneumoniae, the streptococcus pneumoniae of preparation different concns, carry out measuring amplified production sequence after NASBA amplification with its corresponding primer, and its Nucleotide is consistent with target gene.By capture probe and corresponding detection probes, detect, the minimum concentration detecting all can reach 10
-11pM.
Embodiment 7: the primer specificity test of bacillus legionnaires,pneumophila
The scavenger cell of bacillus legionnaires,pneumophila is infected to the gene fragment of Enhancin gene as shown in SEQ ID NO.5 to suddenly change at random, nucleotide sequence after sudden change is as shown in SEQ ID NO.22, in order to narrate conveniently, the scavenger cell that is referred to as bacillus legionnaires,pneumophila infects Enhancin gene fragment interference sequence.
Prepare bacillus legionnaires,pneumophila standard substance described in isocyatic embodiment 5, above-mentioned interference sequence and people DNA, get one of them or mixing between two or three kinds of mixing and be mixed with altogether 7 kinds of different testing samples, every kind of testing sample arranges multiple pipe, 0.5ml without the sterilizing centrifuge tube of RNA enzyme in mark respectively, 20 μ l NASBA amplification reaction systems shown in being formulated as follows, and arrange two without the negative control of RNA enzyme water, 41 ℃ of water-baths 95 minutes simultaneously.Nucleic acid amplification product is for subsequent detection.
The final concentration of NASBA amplification reaction system (20 μ l) is specially:
Testing sample 800 μ M
Primer (the 5th group) 1 μ M
AMV 10U
RNase H 10U
T7 RNA polymerase 10U
Tris/HCl 10mM
Repone K 1mM
BSA 100mg/ml
Dithiothreitol (DTT) 1mM
Nucleoside triphosphate and deoxidation nucleoside triphosphate isoconcentration mixture 200uM
Carry out SDS-PAGE electrophoretic analysis, the reaction tubes that result has shown only to mix bacillus legionnaires,pneumophila standard substance has amplified production, get amplified production and entrust Shanghai Sangon Biological Engineering Technology And Service Co., Ltd to carry out sequential analysis, one section of sequence with capture probe complementation that its sequence has been 5 of nucleotide sequence as shown in SEQ ID NO.5 ' connect.
Embodiment 8: the specificity experiment of other primers
With reference to embodiment 7, nucleic acid fragment by the outer membrane protein A gene of Chlamydia pneumoniae as shown in SEQ ID NO.1, the nucleic acid fragment of OMP26 P6 gene as shown in SEQ ID NO.2, the nucleic acid fragment of mycoplasma pneumoniae attachment proteins P1 gene as shown in SEQ ID NO.3, the interference sequence and the target nucleic acid fragment that after the several base random mutations of the nucleic acid fragment of pneumolysin gene as shown in SEQ ID NO.4, form, people DNA carries out specificity experiment, get one of them or mixing between two or three kinds of mixing and be mixed with altogether 7 kinds of different testing samples, at different reaction tubess, with corresponding primer, increase respectively, SDS-PAGE electrophoretic analysis shows only to have the reaction tubes that has mixed target nucleic acid to have amplified production, with corresponding primer, increase, getting amplified production entrusts Shanghai Sangon Biological Engineering Technology And Service Co., Ltd to carry out sequential analysis, its sequence is one section of target nucleic acid sequence 5 ' connected and capture probe complementary sequence.
Above experimental result illustrates that primer specificity provided by the invention is strong, analyzes reason and is, because external double-stranded DNA is without T7 promoter sequence, can not be amplified, and this has just significantly improved the specificity of NASBA reaction; And the reaction conditions of NASBA is gentle, and shorter than the time of PCR reaction needed, therefore transcribe more faithful to template, further reduced mispairing rate.
The above is only the preferred embodiment of the present invention; it should be pointed out that for those skilled in the art, under the premise without departing from the principles of the invention; can also make some improvements and modifications, these improvements and modifications also should be considered as protection scope of the present invention.
SEQUENCE LISTING
<110> Beijing Haikang DNA Chips Co., Ltd.
<120> method and test kit that detects infectious disease pathogens
<130>MP090693
<160>22
<170>PatentIn version 3.3
<210>1
<211>234
<212>DNA
<213> Chlamydia pneumoniae outer membrane protein A gene 660-893
<400>1
caagggctat aaaggcgttg ctttcccctt gccaacagac gctggcgtag caacagctac 60
tggaacaaag tctgcgacca tcaattatca tgaatggcaa gtaggagcct ctctatctta 120
cagactaaac tctttagtgc catacattgg agtacaatgg tctcgagcaa cttttgatgc 180
tgataacatc cgcattgctc agccaaaact acctacagct gttttaaact taac 234
<210>2
<211>200
<212>DNA
<213> OMP26 P6 gene 17 3-372
<400>2
tttggcggat actctgttgc tgatcttcaa caacgttaca acaccgtata ttttggtttt 60
gataaatacg acatcaccgg tgaatacgtt caaatcttag atgcgcacgc agcatattta 120
aatgcaacgc cagctgctaa agtattagta gaaggtaata ctgatgaacg tggtacacca 180
gaatacaaca tcgcattagg 200
<210>3
<211>127
<212>DNA
<213> mycoplasma pneumoniae attachment proteins P1 gene 3667-3780
<400>3
caccctcggg ggcagtcaga cgatgattac aggcggttcg cctcgaagaa ccctcgacca 60
agccaacctc cagctctgaa cgggggcggg gtgaaggaat gataaggctt caagtggaca 120
aagtgac 127
<210>4
<211>160
<212>DNA
<213> pneumolysin gene 464-623
<400>4
atcccactct tcttgcggtt gatcgtgctc cgatgactta tagtattgat ttgcctggtt 60
tggcaagtag cgatagcttt ctccaagtgg aagaccccag caattcaagt gttcgcggag 120
cggtaaacga tttgttggct aagtggcatc aagattatgg 160
<210>5
<211>158
<212>DNA
The scavenger cell of <213> bacillus legionnaires,pneumophila infects Enhancin gene 406-563
<400>5
ggaaatggtg ttaaacccgg taaatcggat acagttactg tcgaatatac tggtcgtctg 60
attgatggta ccgtttttga cagtaccgaa aaaactggta agccagccac ttttcaggtt 120
tcacaagtga ttccaggatg gacagaggct ttacaatt 158
<210>6
<211>40
<212>DNA
<213> primer Cp-F
<400>6
gatgcaaggt cgcatatgag caagggctat aaaggcgttg 40
<210>7
<211>57
<212>DNA
<213> primer Cp-R
<400>7
aattctaata cgactcacta tagggagaag ggttaagttt aaaatatctg taggtag 57
<210>8
<211>24
<212>DNA
<213> probe Cp-P
<400>8
gaacaaagtc tgcgaccatc aatt 24
<210>9
<211>42
<212>DNA
<213> primer Hi-F
<400>9
gatgcaaggt cgcatatgag tttggcggtt actctgttgc tg 42
<210>10
<211>56
<212>DNA
<213> primer Hi-R
<400>10
aattctaata cgactcacta tagggagaag gcctaatgcg atgttgtatt ctggtg 56
<210>11
<211>26
<212>DNA
<213> probe Hi-P
<400>11
ggtgaatacg ttcaaatctt agatgc 26
<210>12
<211>42
<212>DNA
<213> primer Mp-F
<400>12
gatgcaaggt cgcatatgag agtcagacga tgattgcagg cg 42
<210>13
<211>53
<212>DNA
<213> primer Mp-R
<400>13
aattctaata cgactcacta tagggagaag ggtcactttg ttcgcttgaa gtc 53
<210>14
<211>22
<212>DNA
<213> probe Mp-P
<400>14
atgaaccctc gaccaagcca ac 22
<210>15
<211>42
<212>DNA
<213> primer Sp-F
<400>15
gatgcaaggt cgcatatgag atcccactct tcttgcggtt ga 42
<210>16
<211>55
<212>DNA
<213> primer Sp-R
<400>16
aattctaata cgactcacta tagggagaag gccataatct tgatgccact tagcc 55
<210>17
<211>22
<212>DNA
<213> probe Sp-P
<400>17
gcctggtttg gcaagtagcg at 22
<210>18
<211>43
<212>DNA
<213> primer Lp-F
<400>18
gatgcaaggt cgcatatgag ggaaatggtg ttaaacctgg taa 43
<210>19
<211>56
<212>DNA
<213> primer Lp-R
<400>19
aattctaata cgactcacta tagggagaag gaattgtaaa gcttctgtcc atcctg 56
<210>20
<211>23
<212>DNA
<213> probe Lp-P
<400>20
taagccagcc acttttcagg ttt 23
<210>21
<211>20
<212>DNA
<213> capture probe
<400>21
gatgcaaggt cgcatatgag 20
<210>22
<211>158
<212>DNA
The scavenger cell of <213> bacillus legionnaires,pneumophila infects the interference sequence of Enhancin gene fragment
<400>22
ggaaatgaga gtaaacccgg taaatcggat acagttactg tcgaatatac tggtcgtctg 60
attgatggta ccgtttttga cagtaccgaa aaaactggta agccagccac ttttcaggtt 120
tcacaagtga ttccaggatg gacagaggct ttacaatt 158